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Abstract

Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut1,2,3,4,5, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals2, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

Acknowledgements

We would like to thank A. Murray, G. Guidotti, E. O’Shea, J. Moffitt and B. Stern for insightful comments; M. Delaney for biochemical analyses; C. Daly, M. Clamp and C. Reardon for sequencing support; N. Fierer for providing ITS primers; A. Luong and K. Bauer for technical assistance; J. Brulc and R. Menon for nutritional guidelines; A. Rahman for menu suggestions; A. Must and J. Queenan for nutritional analysis; and our diet study volunteers for their participation. This work was supported by the National Institutes of Health (P50 GM068763), the Boston Nutrition Obesity Research Center (DK0046200), and the General Mills Bell Institute of Health and Nutrition.

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Editorial Summary

Diet can rapidly alter gut microbiome

Diet influences the structure and function of the gut microbiota in the long term, but it is not clear how rapidly the microbiota is affected by short-term dietary change. Peter Turnbaugh and colleagues studied the effect of transition to a diet consisting entirely of either animal products or plant products on the composition and function of the human gut microbiota. They find that the community changes rapidly, within a single day, overwhelming the pre-existing inter-individual differences in microbiota composition to recapitulate expected patterns of composition and metabolic function for carnivorous and herbivorous mammals. The animal-based diet was associated with higher levels of bile-tolerant microorganisms, including the bacterium Bilophila wadsworthia, which has previously been linked to inflammatory bowel disease. The authors also detected intact foodborne fungi, bacteria and viruses in the distal gut.